Target : phosphotyrosine-protein phosphatase *NCBI Gene ID:3798734 *RefSeq#: VBIShiDys99784_1106 *Protein ID (NP or XP #) or Wolbachia#: RefSeq YP_402621.2 *Organism (including strain):Shigella dysenteriae Sd197 (strain: Sd197, serotype: 1) Etiologic Risk Group (see link below):Risk Group 2 (RG2) - Bacterial Agents Including Chlamydia *Background/Disease Information (sort of like the Intro to your Mini Research Write up): Shigella dysenteriae infection: Shigella dysenteriae is a species of bacteria from the Shigella genus. Dysenteriae is the most common cause of epidemic dysentery in condensed populations such as refugee camps. Infection usually occurs through the fecal-oral route. Infection can be transmitted between people unless appropriate hygiene measures are undertaken. Further, Shigella dysenteriae is associated with the development of Hemolytic uremic syndrome, which includes anemia, thrombocytopenia, and renal failure.
Enzyme Assay information (spectrophotometric, coupled assay ?, reagents): Tyrosine phosphorylation and dephosphorylation of proteins play a critical role during many processes of the immune system, from early development to fully differentiated effector function. Since the opposing actions of protein tyrosine kinases (PTKs) and protein tyrosine phosphatases (PTPs) determine the steady state level of tyrosine phosphorylation on a given protein, it is often important for mechanistic studies to determine the specific activities of PTKs and PTPs. Dephosphorylation of the chromogenic substrate pNPP generates p-nitrophenol, which at an alkaline pH has an intense yellow color that can be measured at 405 nm using a spectrophotometer (Read absorbance at 405 nm). http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3097125/ Reagents and Solutions:
-- List cost and quantity of substrate reagents and supplier The experimenters already have some in lab at UT. However, there was no information on the website about the reagents and suppliers.
Structure Available (Using Homology Model):
---- Query Coverage: 98% ---- Max Score:198 ---- Max Ident: 62% ---- Chain used for homology: Chain A, Crystal Structure Of The Tyrosine Phosphatase Wzb From Escherichia Coli K30 In Complex With Sulphate
Image of homology protein (PyMol Chain A showing, everything else were hidden):
Current Inhibitors: Antipain, Aprotinin, Leupeptin, Pepstatin A, and PMSF
Expression Information (has it been expressed in bacterial cells): It had been expressed in E-Coli bacteria and human.
Purification Method:
N/A
*Amino Acid Sequence (paste as text only - not as screenshot or as 'code'):
*GC% Content for gene: 51.9% *CDS Gene Sequence (codon optimized) - copy from output of Primer Design Protocol (paste as text only): *GC% Content for gene (codon optimized):
*NCBI Gene ID:3798734
*RefSeq#: VBIShiDys99784_1106
*Protein ID (NP or XP #) or Wolbachia#: RefSeq YP_402621.2
*Organism (including strain): Shigella dysenteriae Sd197 (strain: Sd197, serotype: 1)
Etiologic Risk Group (see link below): Risk Group 2 (RG2) - Bacterial Agents Including Chlamydia
*Background/Disease Information (sort of like the Intro to your Mini Research Write up):
Shigella dysenteriae infection: Shigella dysenteriae is a species of bacteria from the Shigella genus. Dysenteriae is the most common cause of epidemic dysentery in condensed populations such as refugee camps. Infection usually occurs through the fecal-oral route. Infection can be transmitted between people unless appropriate hygiene measures are undertaken. Further, Shigella dysenteriae is associated with the development of Hemolytic uremic syndrome, which includes anemia, thrombocytopenia, and renal failure.
Essentiality of this protein:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1278947/
Information about this protein and gene:
http://patricbrc.org/portal/portal/patric/Feature?cType=feature&cId=18691279
http://www.ncbi.nlm.nih.gov/gene/?term=RefSeq%20YP_402621.2
Complex of proteins?: N/A
Druggable Target:
protein tyrosine phosphate + H2O = protein tyrosine + phosphate
EC#: 3.1.3.48
Link to BRENDA EC# page:
http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.48
However, Protein-tyrosine-phosphatase of only humans and other species were found. No information about this typical organism was found.
Enzyme Assay information (spectrophotometric, coupled assay ?, reagents):
Tyrosine phosphorylation and dephosphorylation of proteins play a critical role during many processes of the immune system, from early development to fully differentiated effector function. Since the opposing actions of protein tyrosine kinases (PTKs) and protein tyrosine phosphatases (PTPs) determine the steady state level of tyrosine phosphorylation on a given protein, it is often important for mechanistic studies to determine the specific activities of PTKs and PTPs. Dephosphorylation of the chromogenic substrate pNPP generates p-nitrophenol, which at an alkaline pH has an intense yellow color that can be measured at 405 nm using a spectrophotometer (Read absorbance at 405 nm).
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3097125/
Reagents and Solutions:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3097125/
No information from Sigma about reagents costs.
-- link to Sigma (or other company) page for assay or assay reagents (substrates)
http://www.sigmaaldrich.com/catalog/search?interface=All&term=Protein-tyrosine-phosphatase&lang=en®ion=US&focus=product&N=0+220003048+219853269+219853286&mode=match%20partialmax
-- List cost and quantity of substrate reagents and supplier
The experimenters already have some in lab at UT. However, there was no information on the website about the reagents and suppliers.
Structure Available (Using Homology Model):
---- Query Coverage: 98%
---- Max Score:198
---- Max Ident: 62%
---- Chain used for homology: Chain A, Crystal Structure Of The Tyrosine Phosphatase Wzb From Escherichia Coli K30 In Complex With Sulphate
Image of homology protein (PyMol Chain A showing, everything else were hidden):
Current Inhibitors: Antipain, Aprotinin, Leupeptin, Pepstatin A, and PMSF
Expression Information (has it been expressed in bacterial cells):
It had been expressed in E-Coli bacteria and human.
Purification Method:
N/A
*Amino Acid Sequence (paste as text only - not as screenshot or as 'code'):
MAQLKFNSILVVCTGNICRSPIGERLLRKRLPGVKVKSAGVHGLVKHPADATAADVAANH
GVSLEGHAGRKLTAEMARNYDLILAMESEHIAQVTAIAPEVRGKTMLFGQWLEQKEIPDP
YRKSQDAFEHVYGMLERASQEWAKRLSR
*length of your protein in Amino Acids: 148
Molecular Weight of your protein in kiloDaltons using the**Expasy ProtParam**website: 16.385kDA
Molar Extinction coefficient of your protein at 280 nm wavelength:
Ext. coefficient 15595
TMpred graph Image (http://www.ch.embnet.org/software/TMPRED_form.html). Input your amino acid sequence to it.
*CDS Gene Sequence (paste as text only):
AGCGCTTGCTGCGTAAACGTCTGCCAGGCGTAAAAGTCAAATCGGCAGGTGTTCATGGTCTGGTAAAACA
CCCTGCAGATGCGACAGCAGCAGATGTTGCCGCTAATCATGGCGTATCTCTTGAAGGACATGCCGGACGT
AAGCTCACTGCTGAGATGGCACGAAATTACGATCTGATTCTGGCAATGGAGTCGGAACATATTGCTCAGG
TTACCGCAATCGCTCCCGAGGTCCGCGGGAAGACAATGCTGTTTGGGCAATGGCTGGAACAGAAAGAGAT
CCCGGATCCCTATCGTAAAAGTCAGGACGCATTTGAACATGTCTACGGTATGTTGGAGCGCGCCAGTCAG
GAATGGGCGAAGCGCCTCAGCCGGTAA
*GC% Content for gene: 51.9%
*CDS Gene Sequence (codon optimized) - copy from output of Primer Design Protocol (paste as text only):
*GC% Content for gene (codon optimized):